Catcher Raul Chavez was recalled from Triple-A on Saturday to take Barrett's place on the roster.
Barrett was injured while chasing a wild pitch in Friday night's loss to Oakland, falling on a weighted sleeve in the Athletics' on-deck circle.
Blue Jays general manager J.P. Ricciardi says Barrett's shoulder was too swollen for X-rays to reveal the extent of the injury. Barrett was batting .167 with one homer and two RBIs.
Barrett was limited to 30 games last season. He missed six weeks with a sprained elbow in April and May, and had season-ending facial fractures after fouling a ball off his face in July.